A great wealth of information is currently available regarding the role of microbes in the various functions that occur in an aquaponics system. It is necessary to begin identifying the microbes present in aquaponics systems and compare those to populations of microbes that are important in nutrient cycling, plant health, and fish health to optimize production within the system. We examine microbes that interact with plant health. Studies have been conducted to evaluate the food safety aspects of aquaponics produce, specifically assessing the risk of foodborne pathogens in an aquaponics system. This study is a continuation of that evaluation. We investigated whether transfer of microbial flora occur when microbes are or are not present in the media where Romaine lettuce is raised. We found that the diversity of microbial flora is similar regardless of the type of media in which the plants are grown, and if there is a difference of significance, it is a rare event. Therefore, aquaponics systems are safe for growing plants.